Use of culture and molecular analysis to determine the effect of antibiotic treatment on microbial community diversity and abundance during exacerbation in patients with cystic fibrosis

Abstract

Background Anaerobic bacteria are increasingly regarded as important in cystic fibrosis (CF) pulmonary infection. The aim of this study was to determine the effect of antibiotic treatment on aerobic and anaerobic microbial community diversity and abundance during exacerbations in patients with CF. Methods Sputum was collected at the start and completion of antibiotic treatment of exacerbations and when clinically stable. Bacteria were quantified and identified following culture, and community composition was also examined using culture-independent methods. Results Pseudomonas aeruginosa or Burkholderia cepacia complex were detected by culture in 24/26 samples at the start of treatment, 22/26 samples at completion of treatment and 11/13 stable samples. Anaerobic bacteria were detected in all start of treatment and stable samples and in 23/26 completion of treatment samples. Molecular analysis showed greater bacterial diversity within sputum samples than was detected by culture; there was reasonably good agreement between the methods for the presence or absence of aerobic bacteria such as P aeruginosa (k¼0.74) and B cepacia complex (k¼0.92), but agreement was poorer for anaerobes. Both methods showed that the composition of the bacterial community varied between patients but remained relatively stable in most individuals despite treatment. Bacterial abundance decreased transiently following treatment, with this effect more evident for aerobes (median decrease in total viable count 2.3310 7 cfu/g, p¼0.005) than for anaerobes (median decrease in total viable count 3310 6 cfu/g, p¼0.046). Conclusion Antibiotic treatment targeted against aerobes had a minimal effect on abundance of anaerobes and community composition, with both culture and molecular detection methods required for comprehensive characterisation of the microbial community in the CF lung. Further studies are required to determine the clinical significance of and optimal treatment for these newly identified bacteria.Chronic bacterial pulmonary infection with recurrent infective exacerbations results in an irreversible decline in lung function in patients with cystic fibrosis (CF) and early death.

Antibiotic and Anti-Inflammatory Therapies for Cystic Fibrosis

“…The range of microorganisms, particularly bacteria that have been identified in the CF airway, is much wider than previously appreciated (Tunney et al 2008(Tunney et al , 2011. Using molecular techniques, organisms that were previously unculturable, particularly microaerophilic and anaerobic bacteria, have been identified (Lipuma 2012).…”

“…The virulence of these organisms and their complex interaction as an airway microbiome has yet to be fully established. However, there are some studies to suggest that the diversity or the lack of diversity in sputum and BAL from people with CF is associated with more severe and chronic disease, and this may in part be driven by antibiotic therapy (Tunney et al 2011;Zhao et al 2012) Antimicrobial therapy in CF has a long history, and effective treatment of infection is thought to be one of the key advances that have resulted in improved outcomes over the past 50 years for people with CF (Döring et al 2012). Figure 1.…”

“…Treatment of organisms such as Streptococcus species and anaerobic bacteria such as Prevotella, Veillonella, Rothia, and Actinomyces species is not clear (Tunney et al 2011;Zhao et al 2012). There may be changes in how we perceive treatment with antibiotics over the next several years because second-generation sequencing provides more insight into the complex microbiota of the airways in people with CF.…”

Antibiotic Management of Lung Infections in Cystic Fibrosis. I. The Microbiome, Methicillin-Resistant Staphylococcus aureus, Gram-Negative Bacteria, and Multiple Infections

“…However, many bacteria form biofilms in the CF lung that make their eradication difficult (3). In addition, it has also become clear that only a small fraction of the microbes present in the CF airway are being identified with routine laboratory techniques (4,5), and both extended culture methods and molecular techniques have identified organisms that previously were not routinely cultured (6). Traditional antibiotic susceptibility testing performed on planktonic bacteria has been found to be of limited clinical use in chronic airway infection as most bacteria in the CF lung exist in biofilms (7).…”

Directly Sampling the Lung of a Young Child with Cystic Fibrosis Reveals Diverse Microbiota

“…Alternatively, perioperative antibiotic exposure could have limited culture detection of these organisms. In addition, studies in CF (32) and in other conditions (33) have used molecular methods to identify in clinical specimens H. influenzae that was not identified by concurrent culture, as was the case here. In the case of Ralstonia pickettii, which has also been identified previously in CF secretions (30), this species was likely not cultured here as a result of its heterogeneous lung tissue distribution, and its rarity in the only section that was cultured (section 1; Table E3).…”